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Flashcards in Exam 3 Deck (82)
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1

Amino Acids

-Repeating unit of proteins
-Consists of amino group, carboxyl group, hydrogen atom, and variable R group

2

Peptide Bonds

-Chemical bond that connects amino acids in a protein

3

Polypeptide Chain

-Chain of amino acids linked by peptide bonds
-Protein

4

One gene, one polypeptide hypothesis

-Each gene encodes a separate polypeptide chain

5

Sense Codons

-Codon that specifies an amino acid in a protein

6

Degenerate

-Refers to the fact that the genetic code contains more codons than are needed to specify all 20 AAs

7

Synonymous Codons

-Diff codons that specify the same codon

8

Isoaccepting tRNAs

-Diff tRNAs w/ diff anticodons that spcify the same AA

9

Nonoverlapping

-Each nucleotide is a part of only 1 codon and encodes only 1 AA in a protein

10

Reading frame

-Particular way in which a nucleotide sequence is read in groups of 3 nucs (codon) in translation
-Begins w start codon and ends w/ stop codon

11

Initiation/ start codon

-Codon that specifies the 1st AA of protein
-fMet in prok, Met in Euk
-Most commonly AUG

12

Stop/Termination/Nonsense codons

-Codon in mRNA that signals the end of translation
-UAA, UAG, UGA

13

Aminoacyl-tRNA sythetases

-Enzyme that attaches an amino acid to tRNA
-Specific for a particular AA

14

tRNA charging

-Chemical rxn in which an aminoacyl-tRNA sythetase attaches an AA to its corresponding tRNA

15

IF3

-Protein required for the initiation of translation in proks
-Binds to the small subunit of the ribosome and prevents the large subunit from binding during initiation

16

IF1

-Protein required for initiation of translation in proks
-Enhances disociation of the large and small subunits of the ribosome

17

IF2

-Protein required for initiation of translation in proks
-Forms a complex w/ GTP and charged tRNA & delivers charged tRNA to initiator complex

18

30s initiator complex

-Initial complex formed in the initiation of translayion in proks
-Consists of small subunit of ribosome, mRNA, initiator tRNA charged w fMet, GTP, and IFs 1,2, and 3

19

70s initiator complex

-Final complex formed in the initiation of translation in proks
-Small and large ribosomal subunits, mRNA, and intiator tRNA charged w fMet

20

Cap binding complex

-A group of proteins in euks
-Binds to 5' cap and initiates translation
-Aids in exporting mRNA from nucleus to cytoplasm
-Promotes initial/pioneer round of translation

21

Aminoacyl (A) site

-One of 3 sites in a ribosome occupied by a tRNA during translation
-All charged tRNAs w/ expection of initiator tRNAs first enter the A site

22

Peptidyl (P) site

-One of 3 sites in a ribosome occupied by a tRNA during translation
-In elongation stage, tRNAs move from A to P site

23

Exit (E) site

-One of 3 sites in a ribosome occupied by a tRNA during translation
-In elongation stage, tRNA moves from P to E site
---Exits the ribosome

24

Elongation Factor Tu (EF-Tu)

-Protein taking part in the elongation stage of translation
-Forms a complex w/ GTP and charged tRNA
-Delivers charged tRNA to ribosome

25

Elongation Factor Ts (EF-Ts)

-Protein that regenerates EF-Tu in elongation stage of translation

26

Translocation

-Movement of a ribosome along mRNA in the course of translation

27

Elongation Factor G

-EF-G
-Protein that combines w/ GTP and is required for movement of the ribosome along the mRNA during translation

28

Release Factors

-Protein required for termination of translation
-Binds to ribosome when a stop codon is reached and stimulates the release of the polypeptide chain, the tRNA, and the mRNA from the ribsome
-Euk cell requires eRF-1 and eRF-2
-Proks require RF-1, RF-2, and RF-3

29

Structural Genes

-DNA sequence that encodes a protein that fxns in metabolism or biosynthesis or that has a structural role in the cell

30

Constitutive

-A gene that is expressed continually w/o regulation

31

Regulatory elements

-DNA sequence that affects the transcription of other DNA sequences to which it is physically linked

32

Domian

-Functional part of protein

33

Operon

-Set of structural genes in a prok. cell, along with their common promoter and other sequences (operator) that control their transcription

34

Regulator Gene

-Gene associated w an operon in prok cells
-Encode a protein or RNA molecule that fxns in controlling the transcription of one or more structural genes

35

Regulator Protein

-Protein produced by a regulator gene
-Binds to another DNA sequence (operator) and controls the transcription of one or more structural genes

36

Operator

-DNA sequence in an operon of prok cells
-A regulator protein beings to
-Binding affects rate of transcription of structural genes

37

Neg control

-Gene reg in which the binding of a regulator protein to DNA inhibits transcription
-Reg protein= repressor

38

Positive control

-Gene reguation in which binding of a reg protein to DNA stimulates transcription
-reg protein= activator

39

Inducible operons

-Operon in which transcription is normally turned off so that something must occur for transcription to be induced/turned on

40

Repressible Operons

-Operon in which transcription is normally turned on, so that something must happen for transcriotion to be repressed/turned off

41

Inducer

-Substance that stimulates transcription in an inducible system of gene regulations
-Usually a molecule that binds to a repressor protein, alters that repressor so that it cannot bind to DNA and inhibit transcription

42

Allosteric Proteins

-Protein that changes confirmation upon binding w another molecule

43

Corepressor

-Substance that inhibits transcription in a repressible system of gene regulation
-Molecule that binds to a repressor protein and alters it so that the repressor is able to bind to DNA and inhibit transcription

44

Coordinate Induction

-The simultaneous synthesis of several enzymes stimulated by a single environmental factor

45

Partial Diploid

-Prok cells that possess 2 copies of the same genes
--One on chromosome, one on plasmid

46

Catabolite Repression

-System of gene control in prok. operons
-Glucose is used preferentially and the metabolism of other sugas is repressed in the presence of glucose

47

Catabolite Activator Protein (CAP)

-Proteins that fxn in catabolite repression
-When bound w cAMP, CAP binds to the promoter of certain operons and stimulates transcription

48

cAMP

-Modified nucleotide that fxns in catabolite repression
-Low levels of glucose stimulate high levels of cAMP
---cAMP attaches to CAP, which binds to the promoters of certain operons and stimulates transcription

49

Attenuation

-Type of gene regulation in some prok operons
-Transcription is initiated but terminates prematurely b4 transcription of structural genes

50

Attenuator

-Secondary structure that forms in the 5' untranslated region of some operons
-Causes the premature termination of transcription

51

Antiterminator

-Protein or DNA sequence that inhibits the termination of transcription

52

Antisense RNA

-Small RNA mol that bps w a complementary DNA or RNA sequence and affects its fxning
-Control gene expression by binding to sequences on mRNA and inhibiting its translation

53

Riboswitches

-Regulatory sequence in an RNA molecule
-When inducer binds to riboswitch, binding changes the configuration of the RNA molecule and alters the expression of RNA
--Usually by affecting the termination of transcription or translation

54

Structural Genes on the Lac Operon

-Lac Z--> gene that makes B galactosidase enzyme
-Lac Y--> Permease
---Allows lactose into cell
-Lac A--> Transacetylase

55

Lac I

-Regulator gene, encode regulator protein
-Lac I- = nonfunctional repressor protein
-Lac I^s= superrepressor, allolactose cannot bind to it
-Trans
Lac I s> Lac I+ > Lac I-

56

Lac O

-operator
-Cis
-LacO^C= Repressor cannot bind to operator region
Lac O c> Lac O+
*Can transcribe structural genes w or w/o lactose

57

Lac Operon

-Ex of negative inducible operon
-When lactose levels= high, allolactose converted to lactose by B-galactose, binds to repressor protein
---Repressor cannot bind to operator, transcription occurs
-Lactose levels= low, no allolactose, transcription is inhibited
---Repressor can bind to operator

58

DNase I hypersensitivity sites

-Chromatin region that becomes sensitive to digestion by enzyme DNase I

59

Chomatin remodeling complexes

-Complex of proteins that alters chromatin structure w/o acetylating histone proteins

60

Histone code

-Modifications in histone proteins
-Add. or removal of phosphate, methyl, or acetyl groups that encode info affecting how genes are expressed

61

CpG islands

-DNA region that contains many copies of a cytosine base followed by a guanine base
-Often found near transcription start sites in euk DNA
-Cytosine base in CpG commonly methylated when genes are inactive
---Demethylated b4 initiation of transcription
-METHYLATED DNA=REPRESSED TRANSCRIPTION

62

3 processes that affect gene regulation by altering chromatin structure

-Chromatin remodeling
-Modification of histone proteins
-DNA methylation

63

Methylation of histones

-Histone methyltransferases= add CH3 to histones
-Histone Demethylases= remove CH3
-Activates or represses transcription

64

Acetylation of Histones

-Addition stimulates transcription
-CH3CO
-Add by acetyltransferase
-Removed by deacetylases (represses transcription)

65

Arabidopsis and Flowering

-FLD stimulates flowering by deacetylating chromatin around FLC
-FLC inhibits flowering, when acetyl groups removed it is inhibited

66

Mediators

-Complex of proteins that is one of the components of the basal transcription apparatus

67

Insulators

-DNA sequences that blocks or insulates the effect of an enhancer
-Must be located btwn promoter and enhancer to block activity
-May also limit the spread of changes in chromatin structure

68

Response Elements

-DNA sequence shared by promoters or enhancers of several euk genes
-Regulatory proteins can bind to stimulate the coordinate transcription of these genes

69

Regulation of Galactose Metabolism Through Gal4

-Gal4= transcriptional activator protein
-galactose low= genes not transcribed
---High= genes r transcribed and galactose broken down
-Gal4 binds to UASg--> activates transcription needed to metabolize galactose
-Gal4 and Gal80 bind--> prevents transcription when gal=low
-When galactose= present, Gal3 binds to Gal80 so it cant bind to Gal4--> transcription occurs and galactose is metabolized

70

siRNAs scilence transcription by altering chromatin structure

-siRNA combines w protein to create RITS
-Binds to complementary sequence in DNA or RNA molecule in process of being transcribed, repressing transcription by attracting enzymes that methylate histones

71

Bacterial Enhancers

-Element that affects transcription but far from gene its affects
-Binding site 4 proteins to increase rate of transcription
--Do this by causing DNA btwn enhancer and promoter to loop out and interact w one another
-Position independent

72

Trp Operon

-Ex of neg repressible operon
-5' UTR has 4 complementary regions
---1 comp to 2
---2 comp to 3
---3 comp to 4
-----Allows 5' UTR to make 2 secondary structures

73

Attenuation process of Trp Operon

-High levels of tryptophan--> no stalling of ribsome cuz tRNAs are charged
---> Bping of 3 and 4, hairpin followed by Us--> attenuation
-Ribosome partially covers 2 when RNA pol finishes 3, so cannot BP
---3 bps w 4 because it didn't w 2

74

Antiterminator process of Trp Operon

-Low levels of tryptophan--> stalling of ribosome cuz tRNA arent charged
---> Bping of 2 and 3, hairpin not followed by Us--> No attenuation
-Ribosome stalls at trp codons UGG
- 2 and 3 bp because ribosome stuck at 1

75

Combinatorial Control

-Different combinations of activators and repressors determine transcription
--Stimulates interaction of multiple regulatory proteins (activators and repressors) binding to enhancers and scilencers in diff combos

76

3 regions that euk regulatory proteins interact w

1. Core promoter
--Upstream from gene regulating
2. Proximal elements
--Found in reg. promoter, upstream of gene
3. Enhancers and Scilencers
--Proximity-dependent, bind to activators or repressors

77

SWI/SNF complex

-Chromatin remodeling
-Uses energy from hydrolysis of ATP
-Slides or ejects nucleosomes, freeing promoters to bind to transcription factors and RNA pol 4 transcription

78

What does RNA pol do when it encounters nucleosomes? How does this differ for genes of diff transcription levels?

-Highly transcribed genes--> RNA pol ejects histones, nucleosomes reform on DNA behind RNA pol II
-Lowly transcribed genes--> H2A/H2B dimer is ejected, RNA pol moves around histone hexamer, nucleosomes reform behind RNA pol II

79

RNA interference

-A noncoding RNA targets complementary mRNAs w/in a cell for scilencing or degradation
1. miRNAs--> form small hairpins, mRNA unable to be translated
2.siRNAs--> degrades mRNA

80

Dicer

-Endonuclease that cuts the dsRNA into 21-25 bp fragments

81

RISC

-RNA-induced scilencing complex
-Degrades 1 strand of RNA
-Binds to target mRNA and..
----Cleaves and degrades
----Inhibits translation
----Attracts methylases and deacetylases, spreading heterochromatin

82

Wobble

-Occurs at 3rd position
-Multiple mRNA codons can be recognized by the same tRNA